Heh, that's for you to decide XD
I guess since it's unlikely anyone would casually run into any of these it doesn't "need fixing." One of the joys of doom is "getting to places you (seemingly) aren't supposed to get to" so leaving them in intentionally might be kind of fun, even a reward for one, like a screen message for getting up into the rafters or something. Quake 2 had a similar reward IIRC; in one level towards the end if you rocket jumped behind a cistern it said "you crazy rocket jumpers" or something. The single jump sequence break is already inside of a secret, so could already be considered its own reward. As for general game-play, I'm aiming to do a playtest of this new "version 1." After a quick poke around I'm glad to see there's some more health scattered around (There were times where it felt like the crossing Sahara desert between health packs lol!). I haven't gotten to the new "ending" yet so that'll be virgin when I do the video.
Peace!